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Solid-state NMR structure of teixobactin-lipid II

Analyse Solid-state NMR structure of teixobactin-lipid II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
7QGV
Type
protein
Length
64 residues
Chains
8
Method
solid-state nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Teixobactin; Lipid II
Ligands
P1W, 2PO, MUB, NAG

Structure

solid-state nmr · 2 distinct chains · 0% helix, 31% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, DTeixobactinprotein110% helix, 45% strand—
E, F, G, HLipid IIprotein50% helix, 0% strand—

Ligands and binding sites

  • P1W · 3-methylbut-2-en-1-ol · ligand · 12 copies · chains A, B, F, C, D
  • 2PO · Phosphonate · ligand · 8 copies · chains A, B, C, E, D
  • MUB · N-acetyl-alpha-muramic acid · ligand · 4 copies · chains A, E, B, F, H, C, G, D
  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains E, F, H, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

12 interfaces between chains.

  • C–D · 427 Ų buried · 13 hydrogen bonds · protein-protein
  • B–C · 417 Ų buried · 12 hydrogen bonds · protein-protein
  • A–B · 405 Ų buried · 12 hydrogen bonds · protein-protein
  • B–F · 105 Ų buried · 4 hydrogen bonds · protein-protein
  • E–G · 75 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 d-amino, 12 modified, 4 covalent (D-amino acid, nonstandard, covalent ligand).

Compared structures

  • 7QGV · Solid-state NMR structure of Teixobactin-Lipid II. · the same entry in another collection · chain A against A, TM-score 1.00

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